text: The metabolome refers to the complete set of small-molecule (<1.5 kDa) metabolites (such as metabolic intermediates, hormones and other signaling molecules, and secondary metabolites) to be found within a biological sample, such as a single organism. The word was coined in analogy with transcriptomics and proteomics; like the transcriptome and the proteome, the metabolome is dynamic, changing from second to second. Although the metabolome can be defined readily enough, it is not currently possible to analyse the entire range of metabolites by a single analytical method.
  The first metabolite database (called METLIN) for searching fragmentation data from tandem mass spectrometry experiments was developed by the Siuzdak lab at The Scripps Research Institute in 2005. METLIN contains over 450,000 metabolites and other chemical entities, each compound having experimental tandem mass spectrometry data. In 2006, the Siuzdak lab also developed the first algorithm to allow for the nonlinear alignment of mass spectrometry metabolomics data. Called XCMS, where the "X" constitutes any chromatographic technology, it has been developed as an online tool.
  In January 2007, scientists at the University of Alberta and the University of Calgary completed the first draft of the human metabolome. The Human Metabolome Database (HMDB) is perhaps the most extensive public metabolomic spectral database to date and is a freely available electronic database (www.hmdb.ca) containing detailed information about small molecule metabolites found in the human body. It is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education. The database is designed to contain or link three kinds of data:
  # Chemical data,
  # Clinical data and
  # Molecular biology/biochemistry data.
  The database contains 220,945 metabolite entries including both water-soluble and lipid soluble metabolites. Additionally, 8,610 protein sequences (enzymes and transporters) are linked to these metabolite entries. Each MetaboCard entry contains 130 data fields with 2/3 of the information being devoted to chemical/clinical data and the other 1/3 devoted to enzymatic or biochemical data. The version 3.5 of the HMDB contains >16,000 endogenous metabolites, >1,500 drugs and >22,000 food constituents or food metabolites. This information, available at the Human Metabolome Database and based on analysis of information available in the current scientific literature, is far from complete. In contrast, much more is known about the metabolomes of other organisms. For example, over 50,000 metabolites have been characterized from the plant kingdom, and many thousands of metabolites have been identified and/or characterized from single plants.
  Each type of cell and tissue has a unique metabolic ‘fingerprint’ that can elucidate organ or tissue-specific information. Bio-specimens used for metabolomics analysis include but not limit to plasma, serum, urine, saliva, feces, muscle, sweat, exhaled breath and gastrointestinal fluid. The ease of collection facilitates high temporal resolution, and because they are always at dynamic equilibrium with the body, they can describe the host as a whole. Genome can tell what could happen, transcriptome can tell what appears to be happening, proteome can tell what makes it happen and metabolome can tell what has happened and what is happening.